[chimerax-users] Converting Chimera movie script
Vid Sustar
vid.sustar at abo.fi
Fri Jun 26 15:50:51 PDT 2020
The following bug report has been submitted:
Platform: Linux-5.3.0-61-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Hello!
I have tried to adapt the cliping script from
http://www.rbvi.ucsf.edu/chimera/data/movie-howto-mar2012/scripts/clip.cmd
to work in ChimeraX (because my structure is too big, to be loaded properly in earlier Chimera)
I tried to convert the old commands to the ChimeraX, but I get an error in the line "clip front -0.5 120": Expected a keyword
Please advise me how to change the code to work with ChimeraX to create a movie
or to simply save a series of images of cliped planes
Best regards,
Vid Sustar
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.py
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 365, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 48, in open
return open_python_script(session, data, file_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/scripting.py", line 82, in open_python_script
_exec_python(session, code, argv)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/scripting.py", line 59, in _exec_python
exec(code, sandbox.__dict__)
File "clip2.py", line 3, in <module>
ModuleNotFoundError: No module named 'chimera'
ModuleNotFoundError: No module named 'chimera'
File "clip2.py", line 3, in
See log for complete Python traceback.
> ui tool show Shell
/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
> select up
Nothing selected
> open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.py
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 365, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 48, in open
return open_python_script(session, data, file_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/scripting.py", line 82, in open_python_script
_exec_python(session, code, argv)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/scripting.py", line 59, in _exec_python
exec(code, sandbox.__dict__)
File "clip2.py", line 3, in <module>
ModuleNotFoundError: No module named 'chimera'
ModuleNotFoundError: No module named 'chimera'
File "clip2.py", line 3, in
See log for complete Python traceback.
> open /home/user/MASTERS/Chimera_files/PythonScripts/writeMol2.py
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 365, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 48, in open
return open_python_script(session, data, file_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/scripting.py", line 82, in open_python_script
_exec_python(session, code, argv)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/scripting.py", line 59, in _exec_python
exec(code, sandbox.__dict__)
File "writeMol2.py", line 2, in <module>
ModuleNotFoundError: No module named 'chimera'
ModuleNotFoundError: No module named 'chimera'
File "writeMol2.py", line 2, in
See log for complete Python traceback.
> help help:user
> open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.py
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 365, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 48, in open
return open_python_script(session, data, file_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/scripting.py", line 82, in open_python_script
_exec_python(session, code, argv)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/scripting.py", line 59, in _exec_python
exec(code, sandbox.__dict__)
File "clip2.py", line 4, in <module>
ImportError: cannot import name 'runCommand' from 'chimerax' (unknown
location)
ImportError: cannot import name 'runCommand' from 'chimerax' (unknown
location)
File "clip2.py", line 4, in
See log for complete Python traceback.
> open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc
> open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb
> select :wat
157584 atoms, 157584 bonds, 1 model selected
> hide sel target a
> select ~sel
37869 atoms, 34860 bonds, 1 model selected
> surface sel
> color (#!1 & sel) white
> select ::name="OQL"
2380 atoms, 2520 bonds, 1 model selected
> color (#!1 & sel) red
> select ::name="ONC"
4200 atoms, 3920 bonds, 1 model selected
> color (#!1 & sel) blue
> select ::name="NP"
2869 atoms, 1 model selected
> color (#!1 & sel) yellow
> lighting flat
> lighting shadows false
> graphics silhouettes false
> movie record supersample 3
> clip front -0.5
> wait
wait requires a frame count argument unless motion is in progress
> movie encode clip.mp4 bitrate 200
Movie encoding failed because no images were recorded.
> close session
> open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc
> open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb
> select :wat
157584 atoms, 157584 bonds, 1 model selected
> hide sel target a
> select ~sel
37869 atoms, 34860 bonds, 1 model selected
> surface sel
> color (#!1 & sel) white
> select ::name="OQL"
2380 atoms, 2520 bonds, 1 model selected
> color (#!1 & sel) red
> select ::name="ONC"
4200 atoms, 3920 bonds, 1 model selected
> color (#!1 & sel) blue
> select ::name="NP"
2869 atoms, 1 model selected
> color (#!1 & sel) yellow
> lighting flat
> lighting shadows false
> graphics silhouettes false
> movie record supersample 3
> clip front -0.5 120
Expected a keyword
> close session
> open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc
> open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb
> select :wat
157584 atoms, 157584 bonds, 1 model selected
> hide sel target a
> select ~sel
37869 atoms, 34860 bonds, 1 model selected
> surface sel
> color (#!1 & sel) white
> select ::name="OQL"
2380 atoms, 2520 bonds, 1 model selected
> color (#!1 & sel) red
> select ::name="ONC"
4200 atoms, 3920 bonds, 1 model selected
> color (#!1 & sel) blue
> select ::name="NP"
2869 atoms, 1 model selected
> color (#!1 & sel) yellow
> lighting flat
> lighting shadows false
> graphics silhouettes false
> windowsize 200 150
> copy file clip.jpg
Unknown command: copy file clip.jpg
> copy
Unknown command: copy
> save /home/user/Desktop/image1.png supersample 3
> movie record
Already recording a movie
> open /home/user/Desktop/gbpmovie.cxc
No such file/path: /home/user/Desktop/gbpmovie.cxc
> close session
> open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc
> open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb
> select :wat
157584 atoms, 157584 bonds, 1 model selected
> hide sel target a
> select ~sel
37869 atoms, 34860 bonds, 1 model selected
> surface sel
> color (#!1 & sel) white
> select ::name="OQL"
2380 atoms, 2520 bonds, 1 model selected
> color (#!1 & sel) red
> select ::name="ONC"
4200 atoms, 3920 bonds, 1 model selected
> color (#!1 & sel) blue
> select ::name="NP"
2869 atoms, 1 model selected
> color (#!1 & sel) yellow
> lighting flat
> lighting shadows false
> graphics silhouettes false
> movie record supersample 3
Already recording a movie
> movie stop
> movie record supersample 3
> movie stop
> movie stop
Not currently recording
> close session
> open /home/user/MASTERS/Chimera_files/PythonScripts/clip2.cxc
> open /home/user/MASTERS/Chimera_files/testPDBfiles/Sys1nanopart.pdb
> select :wat
157584 atoms, 157584 bonds, 1 model selected
> hide sel target a
> select ~sel
37869 atoms, 34860 bonds, 1 model selected
> surface sel
> color (#!1 & sel) white
> select ::name="OQL"
2380 atoms, 2520 bonds, 1 model selected
> color (#!1 & sel) red
> select ::name="ONC"
4200 atoms, 3920 bonds, 1 model selected
> color (#!1 & sel) blue
> select ::name="NP"
2869 atoms, 1 model selected
> color (#!1 & sel) yellow
> lighting flat
> lighting shadows false
> graphics silhouettes false
> movie record supersample 3
> clip front -0.5 120 ; wait 120 ; movie encode clip.mp4 bitrate 200
Expected a keyword
> help help:contact.html
OpenGL version: 3.3.0 NVIDIA 440.100
OpenGL renderer: GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GL63 8SE
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz
Cache Size: 9216 KB
Memory:
total used free shared buff/cache available
Mem: 31G 6.1G 18G 662M 6.6G 24G
Swap: 2.0G 0B 2.0G
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:3e9b]
Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:126a]
Kernel driver in use: i915
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: clip2.cxc
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